[galaxy-dev] core dump after trying to view data
Hello Galaxy Buddies, I am having a problem with run.sh core dumping. It happens when I try to view data (click on the eye) for a large text file of results. It doesn't happen when viewing data of a smaller size and it executes jobs fine. Here is the server's output. Starting server in PID 30831. serving on http://127.0.0.1:8000 127.0.0.1 - - [05/Apr/2013:15:08:26 -0400] GET / HTTP/1.1 200 - - Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11 127.0.0.1 - - [05/Apr/2013:15:08:26 -0400] GET /root/tool_menu HTTP/1.1 200 - http://localhost:8000/; Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11 127.0.0.1 - - [05/Apr/2013:15:08:26 -0400] GET /history HTTP/1.1 200 - http://localhost:8000/; Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11 127.0.0.1 - - [05/Apr/2013:15:08:27 -0400] GET /history/get_display_application_links HTTP/1.1 200 - http://localhost:8000/history; Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11 127.0.0.1 - - [05/Apr/2013:15:08:30 -0400] GET /datasets/1e8ab44153008be8/display/?preview=True HTTP/1.1 200 - http://localhost:8000/history; Mozilla/5.0 (X11; Linux x86_64; rv:10.0.11) Gecko/20121116 Firefox/10.0.11 run.sh: line 78: 30831 Segmentation fault (core dumped) python ./scripts/paster.py serve universe_wsgi.ini $@ [jje16@rgs06 galaxy-dist]$ I am running Galaxy on Red Hat Linux under the most recent stable build. If it matters, it submits jobs to a cluster using the drmaa job runner. [jje16@rgs06 galaxy-dist]$ hg summary parent: 9232:9264cf7148c0 Added tag release_2013.04.01 for changeset 75f09617abaa branch: stable commit: 85 unknown (clean) update: (current) [jje16@rgs06 galaxy-dist]$ any ideas on where to look? thanks much, Jason Jason Evans jason.j.ev...@gmail.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] BioBlend: Problem Running Example file
Perhaps your json is empty. Is there anything in that string? Jason On Mar 8, 2013, at 11:23 AM, Sytchev, Ilya isytc...@hsph.harvard.edu wrote: JSONDecodeError will be raised if the given JSON document is not valid. http://simplejson.readthedocs.org/en/latest/ Ilya From: Rob Leclerc robert.lecl...@gmail.com Date: Friday, March 8, 2013 12:01 AM To: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu Subject: [galaxy-dev] BioBlend: Problem Running Example file I had trouble running blend4j, so I tried to jump into python (a language I have little experience with). I tried running the example run_import_workflow.py % python run_imported_workflow.py http://localhost:8080 8c25bc83f6f9e4001dd21eb7b64f063f but I get an error: Initiating Galaxy connection Importing workflow Creating data library 'Imported data for API demo' Traceback (most recent call last): File run_imported_workflow.py, line 53, in module library_dict = gi.libraries.create_library(library_name) File build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/libraries/__init__.py, line 27, in create_library File build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/client.py, line 53, in _post File build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/__init__.py, line 132, in make_post_request File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/requests-1.1.0-py2.7.egg/requests/models.py, line 604, in json return json.loads(self.text or self.content) File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/__init__.py, line 454, in loads return _default_decoder.decode(s) File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py, line 374, in decode obj, end = self.raw_decode(s) File /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py, line 393, in raw_decode return self.scan_once(s, idx=_w(s, idx).end()) simplejson.scanner.JSONDecodeError: Expecting value: line 1 column 1 (char 0) Is there anything I am missing from the stock configuration which would cause this not to run out of the box? Cheers, Rob ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] upload of local file ends up with a broken pipe.
Greetings Carl,
Thanks for your response. I pulled and updated and the broken pipe error still
occurs. I am using revision 9fd7fe0c5712 .
The error was regular, but now seems intermittent. I've been trying to
reproduce it and could only see it cause an error once.
I don't think it was doing this before, but the upload completes properly now.
It still gives an error in the output, but finishes and the data is there.
thanks again,
Jason
Jason Evans
jason.j.ev...@gmail.com
On Mar 7, 2013, at 9:52 AM, Carl Eberhard carlfeberh...@gmail.com wrote:
Hello, Jason
At which revision of galaxy-central or galaxy-dist is your installation?
Does this happen intermittently or regularly (with every upload)?
Thanks,
Carl
On Mon, Feb 25, 2013 at 1:49 PM, Jason Evans jason.j.ev...@gmail.com wrote:
I am having difficulties with my local instance of Galaxy on Mac OS X. Upon
using the local file upload tool I get an error resultant of a broken pipe in
python.
The command-line output is as follows.
127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] GET /history HTTP/1.1 500 -
http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0
(Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko)
Version/6.0.2 Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 50438)
Traceback (most recent call last):
File
/Users/jjevans/Work/Tools/Galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 641, in __init__
self.finish()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 694, in finish
self.wfile.flush()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py,
line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] GET
/api/histories/2a56795cad3c7db3 HTTP/1.1 200 -
http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel Mac OS X
10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to
handler 'upload_handler'
My instance has worked for this task in the past, but I'm not sure if it has
been since my last Galaxy update or perhaps something with my configuration
changed.
thanks for your help,
Jason
___
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___
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and other Galaxy lists, please use the interface at:
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[galaxy-dev] upload of local file ends up with a broken pipe.
I am having difficulties with my local instance of Galaxy on Mac OS X. Upon
using the local file upload tool I get an error resultant of a broken pipe in
python.
The command-line output is as follows.
127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] GET /history HTTP/1.1 500 -
http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0
(Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko)
Version/6.0.2 Safari/536.26.17
Exception happened during processing of request from ('127.0.0.1', 50438)
Traceback (most recent call last):
File
/Users/jjevans/Work/Tools/Galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 641, in __init__
self.finish()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py,
line 694, in finish
self.wfile.flush()
File
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py,
line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] GET /api/histories/2a56795cad3c7db3
HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (Macintosh; Intel
Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2
Safari/536.26.17
galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to handler
'upload_handler'
My instance has worked for this task in the past, but I'm not sure if it has
been since my last Galaxy update or perhaps something with my configuration
changed.
thanks for your help,
Jason
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
